Behind Blue Eyes
by WriterLola24
Summary: Neal goes in undercover to take down the bad guy and save the day, it was just another case, until it wasn't. What happens when Neal loses years of his life? Will Peter finally find all the unanswered questions about Neal's past? Stay tuned to find out…
1. Chapter 1

Hey guys! This is my first White Collar fanfic but I felt a need to write it. I LOVE White Collar and am super upset it's over. However, I am even more upset that we never knew more about Neal's backstory! Who was his mother? What was it like growing up in witness protection? Did he have anyone else? What was the final straw that turned him to crime? Who taught him along the way? SO many questions! Well… here is my version to the answers…

 **WARNINGS: DEATH, BLOOD, ABUSE...probably more.**

Chapter One

Just Another Day at Work

Neal held the dark leather case close as he strolled through the glass door. His FBI watch rested reassuringly against his wrist as he was scanned for bugs by a fairly attractive woman in a black dress.

"Now that you know we are alone, how about we get down to business?" Neal says in slight annoyance. He knows he should be on his "A" game since its a case, however he feels slightly ill and this was his third undercover opp in a row. He was tired.

"Why the rush Mr. Carlton?" the woman asks flirtatiously. Neal restrains himself from rolling his eyes. This woman was handsy from the start, another thing he was tiring of.

"I have dinner plans with my wife Ms. Johnson. I wouldn't want to disappoint her on our anniversary," he easily lies. The woman pouts before seemingly accepting his excuse. She turns on her ridiculously tall heels and grabs a silver case just behind the marble counter she stood in front of.

"I'll show you mine if you show me yours," she smiles and winks at Neal. This time he can't help the forced smile that takes his face, it was better than an eye roll at least. He lays his case next to hers and flips the metal latches and looks to her expectantly. She does the same and they open the cases at the same time. She cooes at the full case of money Neal holds and Neal releases a breath of relief at the sight of the painting he was to recover.

"Well, it would appear that everything is in order," Neal says the practiced line in confirmation so the team could move in and end this, however it didn't quite go as planned.

The FBI moved in but Neal missed the gun tucked under the painting. The woman, Ms. Johnson, held it to his temple while pulling him close to her.

"I'm sorry to say that you won't be making it to that dinner Mr. Carlton," she hisses into his ear. Neal suddenly wishes he were nicer to the woman, or that he had at least checked the case.

"Lower your weapon now!" Peter bellowed in warning. The woman did something that set everyone on edge, she laughed.

"I suggest you lower yours agent, or I shoot your partner where we stand," she threatens. Neal's eyes catch Peters and fear strikes both men.

"You don't want to do that," Diane says from behind the woman.

"And why not? If you're here, you know I killed one man. Why not make it two?" she threatens turning so that her back was to the counter and Neal's body shielded hers.

"Look, I can help you. We can figure out a deal, a way to make this better. However, if you shoot him, then I will personally make sure you go away for a long time," Peter promises. The woman ponders for a moment before nodding.

"Okay," she says beginning to lower her gun. Peter cautiously steps forward but she raises her arm quickly in attempt to fire. Time slows as Neal quickly turns and pulls her arm toward himself. The bullet hits him center mass and throws him into the counter where his head hits with a sickening crack. Peter leaps forward to grab the woman's gun but she fires again, this time the bullet hits Neal in the head. Before she can make a third, Diane takes her out with a single shot through the chest. That was three shots, two of which were in Neal Caffrey.

"AGENT DOWN ALL UNITS MOVE IN, I NEED THE PARAMEDICS STAT!" Peter commands. He rushes to his partners side and hovers over his paling body. He nearly cries when his eyes meet Neals, still open.

"Hey buddy, can you move your fingers for me?" Peter nearly begs. Neal looks at him confused before grabbing Peters hand and saying "Yea." Peter shakes his head vigorously.

"No Neal, don't try to talk right now. You stay awake but try not to move your head or face," Peter pleads. Neal looks at him in further confusion. Peter avoids his gaze and presses his free hand to the bleeding wound on Neals chest.

"Why?" Neal asked, then he felt blood in his eye. His hand shakily rose to it before Peter intercepted it from going any further.

"I was shot t-twice wasn't I?" He asks voice wavering. Peter chokes back a sob that suddenly rose to his throat.

"It'll be okay buddy, you're going to be fine. Don't worry," Peter says grasping Neals hand. Neals body begins to shake just as the medics arrive, he was going into shock.

The medics are able to get him onto a stretcher after his body stills and rush out of the building. Peter followed closely, his hand grasping Neals like a lifeline.

"He was just awake a moment ago, moving his hand and talking," Peter says to no one in particular. The female medic looks to him and gives a reassuring look before telling him it was a good thing he still had function and that they would do their best. Peter was pushed out the ambulance and forced to follow behind as they began attaching all sorts of devices to Neal. He gave little protest, as time was of the essence, and sped the whole way behind the ambulance.


	2. Chapter 2

I apologize for any wrong terminology or "unrealistic" events in this chapter as I am neither a doctor nor medical student, so please bear with me. I also LOVE feedback and wouldn't be opposed to hear your own predictions or ideas about Neal's history or where this story will/should go.

Chapter Two

Bad News

Peter was forced to the waiting room as Neal had been rushed to surgery upon entering the building. He sat stiffly in the plastic chair and stared intently at the wall. _Neal had been shot. Twice. His partner was in critical condition. His friend could die._ Peter couldn't help the guilt that consumed him. Neal hadn't wanted to take on this mission so quickly, he had wanted to wait but Peter insisted. He knew how tired Neal was, that he was feeling unwell, but he wanted to get the mission over with before the weekend, so they could all go their separate ways until Monday. _This was his fault, he shouldn't have pushed Neal into doing it._ Peter was so lost in his own mind that he didn't notice the figure who sat beside him, until they took his hand.

"Hi Hon," Elizabeth Burke said softly. Peter jumped slightly before releasing a breath of relief.

"Hi Hon," Peter returned, he suddenly felt a fresh wave of tears. Peter thought he had cried every last one, but as El wiped a stray he realized that he may never stop crying. Peter Burke was a strong agent and tough man, but every time he closed his eyes he saw his partner laying at his feet with blood surrounding him. Peter would never escape that image, or the feeling of Neal's blood on his hands.

"We're going to get through this you know," El said reassuringly. Her relationship with the conman was a strained one, but she knew how much her husband cared for him and despite it all cared for him too.

"How are you here?" Peter asked, he had forgotten to message El since- well, everything.

"Jones and Diana picked me up, they were worried," she said. Peter nodded unable to speak. Elizabeth pulled him closer so that she could hug him reassuringly.

"I don't know if he will make it, El. There was so much blood and he was- he-he c-c-," Peter never finished his sentence as a sob overcame him. It felt like time had stood still as he glimpsed into a future without Neal Caffrey. _No more hat flipping. No more "innocent" smiles. No more laughter. No more bickering. No more Neal._ Peter promised himself that if Neal pulled through he wouldn't waste another moment to have a real heart-to-heart with his friend. He never once said " _I care about you,"_ or " _you're my best friend."_ It's true that you never know how much a person can mean to you until they're gone, or could be.

It felt like hours he sat there with Elizabeth simply holding him. Then time may have literally stopped when Peter heard, "family of Neal Caffrey."

Peter nearly tipped the chair in his rush to stand.

"I'm-I'm Neals guardian," Peter said, it wasn't a lie but it also wasn't the entire truth. _God Neal was rubbing off on him._

"Mr. Caffrey just got out of surgery. The bullet taken center mass was a simple penetrating wound that went through-and through, with minor complications and luckily no vital organs hit, we were then able to focus on our main concern which was the skull piercing. This time the bullet caused a perforating wound. Therefore, we had to perform an emergency craniotomy before the bullet had any possibility of moving. Mr. Caffrey is a lucky man, the gun used seems to have malfunctioned on the second bullet essentially stopping it from penetrating too deep into the frontal lobe. We were able to remove the bullet, however I must prepare you," the doctor sits down beside Peter who had nearly fallen into the chair after hearing Neal was still alive, "this is only the beginning of a long recovery. We still have to monitor brain swelling, possible neurological damage, psychological trauma...Mr. Caffrey is not entirely out of the woods yet. However, off the record I will say that he is one hell of a fighter." Peter let out a shadow of a smile at that. _Yes, Neal was a fighter._

"Can we see him?" Elizabeth asked. The doctor looked to her and kindly said, "He is still in the ICU, I expect him to remain there at least until current swelling goes down." Elizabeth gave a look of disappointment and Peters shoulders sagged a bit.

"Please sir, I almost watched him die in my arms protecting me. I only want to see him for a moment at the least," Peter pleaded finding his voice. He heard a slight gasp and felt El's hand on his shoulder. She didn't know Neal nearly died saving him. The doctor pondered, he was an elder man who had seen it all in his years of practice. It was nice to see a (almost) happy end.

"I will allow you an hour today, however I do not want to startle or push Mr. Caffrey. His body has taken quite a bit of trauma and he is heavily sedated. Until he wakes, we remain unsure of his condition and I do not wish to further antagonize his limits. He has been through two major surgeries in the past 6 hours and we cannot have any setbacks," he warned. Peter nodded, he would do anything at this point. The doctor seemed satisfied enough and led them to Neal's room.

It was dark except for the many blinking lights surrounding the hospital bed. Peter felt a surge of relief and nausea upon finally seeing Neal. There was a thick white bandage going around his newly shaven head, and he had wires and tubes in every possible place. The only comfort to Peter was the steady beep of the heart rate monitor. Peter cautiously walked over to Neal and took his hand, even it had an IV so he was careful to only cradle Neal's limp fingers. The young man looked even younger surrounded by all of the machines. His skin was hued nearly grey and his lips returning from a blue.

"How long was he gone?" Peter asked, surprisingly strong.

"The longest was almost 6 minutes," the doctor answered solemnly.

"How many times?" Peter asked weaker.

"Twice on the way and once here," he replied, "as I've said before Agent Burke, Neal Caffrey is one hell of a fighter."

"Yea, he is," Peter responded with tears in his eyes. Neals heart had stopped three times and one of those had almost claimed him.

"I will leave you be, I expect that you will stay. However I ask that you remember this is a marathon, Agent Burke, not a race. It will take quite a bit of time and patience," the man said before finally departing. Peter heard him, but the very last thought on his mind was leaving Neal. He never wanted him out of his sight again.

"I'll tell June, Mozzie and the team," El said leaving Peter alone with Neal. He had forgotten about everyone else, Neal had been his top priority. Now, the doctors words echoed in his head. _Neal definitely wouldn't wake today, probably not even tomorrow_. Despite the warning, Peter wasn't sure if he could physically leave his partner again.


End file.
